package org.cbioportal.legacy.web;

import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf;

import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.ArrayList;
import java.util.List;
import org.cbioportal.legacy.model.DiscreteCopyNumberData;
import org.cbioportal.legacy.model.Gene;
import org.cbioportal.legacy.model.meta.BaseMeta;
import org.cbioportal.legacy.service.DiscreteCopyNumberService;
import org.cbioportal.legacy.web.config.TestConfig;
import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberEventType;
import org.cbioportal.legacy.web.parameter.DiscreteCopyNumberFilter;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.hamcrest.Matchers;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
import org.springframework.boot.test.mock.mockito.MockBean;
import org.springframework.http.MediaType;
import org.springframework.security.test.context.support.WithMockUser;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.MockMvc;
import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
import org.springframework.test.web.servlet.result.MockMvcResultMatchers;

@RunWith(SpringJUnit4ClassRunner.class)
@WebMvcTest
@ContextConfiguration(classes = {DiscreteCopyNumberController.class, TestConfig.class})
public class DiscreteCopyNumberControllerTest {

  private static final String TEST_MOLECULAR_PROFILE_STABLE_ID_1 =
      "test_molecular_profile_stable_id_1";
  private static final String TEST_SAMPLE_STABLE_ID_1 = "test_sample_stable_id_1";
  private static final int TEST_ENTREZ_GENE_ID_1 = 1;
  private static final int TEST_ALTERATION_1 = 1;
  private static final String TEST_ANNOTATION_JSON_1 =
      "{\"columnName\":{\"fieldName\":\"fieldValue\"}}";
  private static final String TEST_HUGO_GENE_SYMBOL_1 = "test_hugo_gene_symbol_1";
  private static final String TEST_TYPE_1 = "test_type_1";
  private static final String TEST_CYTOBAND_1 = "test_cytoband_1";
  private static final String TEST_CHROMOSOME_1 = "test_chromosome_1";
  private static final String TEST_MOLECULAR_PROFILE_STABLE_ID_2 =
      "test_molecular_profile_stable_id_2";
  private static final String TEST_SAMPLE_STABLE_ID_2 = "test_sample_stable_id_2";
  private static final int TEST_ENTREZ_GENE_ID_2 = 2;
  private static final int TEST_ALTERATION_2 = 2;
  private static final String TEST_HUGO_GENE_SYMBOL_2 = "test_hugo_gene_symbol_2";
  private static final String TEST_TYPE_2 = "test_type_2";
  private static final String TEST_CYTOBAND_2 = "test_cytoband_2";
  private static final String TEST_CHROMOSOME_2 = "test_chromosome_2";
  private static final String TEST_SAMPLE_LIST_ID = "test_sample_list_id";
  private static final int TEST_NUMBER_OF_SAMPLES_1 = 6;
  private static final int TEST_NUMBER_OF_SAMPLES_WITH_ALTERATION_IN_GENE_1 = 4;
  private static final int TEST_NUMBER_OF_SAMPLES_2 = 10;
  private static final int TEST_NUMBER_OF_SAMPLES_WITH_ALTERATION_IN_GENE_2 = 8;

  @MockBean private DiscreteCopyNumberService discreteCopyNumberService;

  private ObjectMapper objectMapper = new ObjectMapper();

  @Autowired private MockMvc mockMvc;

  @Test
  @WithMockUser
  public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdDefaultProjection()
      throws Exception {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList = createExampleDiscreteCopyNumberData();

    Mockito.when(
            discreteCopyNumberService.getDiscreteCopyNumbersInMolecularProfileBySampleListId(
                Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(discreteCopyNumberDataList);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number")
                .param("sampleListId", TEST_SAMPLE_LIST_ID)
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .accept(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].alteration").value(TEST_ALTERATION_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].namespaceColumns.columnName.fieldName")
                .value("fieldValue"))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].alteration").value(TEST_ALTERATION_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist());
  }

  @Test
  @WithMockUser
  public void getDiscreteCopyNumbersWithoutAnnotationJson() throws Exception {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList = createExampleDiscreteCopyNumberData();
    discreteCopyNumberDataList.get(0).setAnnotationJson(null);
    Mockito.when(
            discreteCopyNumberService.getDiscreteCopyNumbersInMolecularProfileBySampleListId(
                Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(discreteCopyNumberDataList);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number")
                .param("sampleListId", TEST_SAMPLE_LIST_ID)
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .accept(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].namespaceColumns").doesNotExist());
  }

  @Test
  @WithMockUser
  public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdDetailedProjection()
      throws Exception {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList =
        createExampleDiscreteCopyNumberDataWithGenes();

    Mockito.when(
            discreteCopyNumberService.getDiscreteCopyNumbersInMolecularProfileBySampleListId(
                Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(discreteCopyNumberDataList);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number")
                .param("sampleListId", TEST_SAMPLE_LIST_ID)
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .param("projection", "DETAILED")
                .accept(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].alteration").value(TEST_ALTERATION_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol")
                .value(TEST_HUGO_GENE_SYMBOL_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.type").value(TEST_TYPE_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].alteration").value(TEST_ALTERATION_2))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol")
                .value(TEST_HUGO_GENE_SYMBOL_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.type").value(TEST_TYPE_2));
  }

  @Test
  @WithMockUser
  public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdMetaProjection()
      throws Exception {

    BaseMeta baseMeta = new BaseMeta();
    baseMeta.setTotalCount(2);

    Mockito.when(
            discreteCopyNumberService.getMetaDiscreteCopyNumbersInMolecularProfileBySampleListId(
                Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(baseMeta);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number")
                .param("sampleListId", TEST_SAMPLE_LIST_ID)
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .param("projection", "META"))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(MockMvcResultMatchers.header().string(HeaderKeyConstants.TOTAL_COUNT, "2"));
  }

  @Test
  @WithMockUser
  public void fetchDiscreteCopyNumbersInMolecularProfileDefaultProjection() throws Exception {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList = createExampleDiscreteCopyNumberData();

    Mockito.when(
            discreteCopyNumberService.fetchDiscreteCopyNumbersInMolecularProfile(
                Mockito.anyString(),
                Mockito.anyList(),
                Mockito.anyList(),
                Mockito.anyList(),
                Mockito.anyString()))
        .thenReturn(discreteCopyNumberDataList);

    DiscreteCopyNumberFilter discreteCopyNumberFilter = createDiscreteCopyNumberFilter();

    mockMvc
        .perform(
            MockMvcRequestBuilders.post(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number/fetch")
                .with(csrf())
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .accept(MediaType.APPLICATION_JSON)
                .contentType(MediaType.APPLICATION_JSON)
                .content(objectMapper.writeValueAsString(discreteCopyNumberFilter)))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].alteration").value(TEST_ALTERATION_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].alteration").value(TEST_ALTERATION_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist());
  }

  @Test
  @WithMockUser
  public void fetchDiscreteCopyNumbersInMolecularProfileDetailedProjection() throws Exception {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList =
        createExampleDiscreteCopyNumberDataWithGenes();

    Mockito.when(
            discreteCopyNumberService.fetchDiscreteCopyNumbersInMolecularProfile(
                Mockito.anyString(),
                Mockito.anyList(),
                Mockito.anyList(),
                Mockito.anyList(),
                Mockito.anyString()))
        .thenReturn(discreteCopyNumberDataList);

    DiscreteCopyNumberFilter discreteCopyNumberFilter = createDiscreteCopyNumberFilter();

    mockMvc
        .perform(
            MockMvcRequestBuilders.post(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number/fetch")
                .with(csrf())
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .param("projection", "DETAILED")
                .accept(MediaType.APPLICATION_JSON)
                .contentType(MediaType.APPLICATION_JSON)
                .content(objectMapper.writeValueAsString(discreteCopyNumberFilter)))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].alteration").value(TEST_ALTERATION_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol")
                .value(TEST_HUGO_GENE_SYMBOL_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.type").value(TEST_TYPE_1))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].molecularProfileId")
                .value(TEST_MOLECULAR_PROFILE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].alteration").value(TEST_ALTERATION_2))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol")
                .value(TEST_HUGO_GENE_SYMBOL_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.type").value(TEST_TYPE_2));
  }

  @Test
  @WithMockUser
  public void fetchDiscreteCopyNumbersInMolecularProfileMetaProjection() throws Exception {

    BaseMeta baseMeta = new BaseMeta();
    baseMeta.setTotalCount(2);

    Mockito.when(
            discreteCopyNumberService.fetchMetaDiscreteCopyNumbersInMolecularProfile(
                Mockito.anyString(), Mockito.anyList(), Mockito.anyList(), Mockito.anyList()))
        .thenReturn(baseMeta);

    DiscreteCopyNumberFilter discreteCopyNumberFilter = createDiscreteCopyNumberFilter();

    mockMvc
        .perform(
            MockMvcRequestBuilders.post(
                    "/api/molecular-profiles/test_molecular_profile_id/discrete-copy-number/fetch")
                .with(csrf())
                .contentType(MediaType.APPLICATION_JSON)
                .content(objectMapper.writeValueAsString(discreteCopyNumberFilter))
                .param(
                    "discreteCopyNumberEventType",
                    DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name())
                .param("projection", "META"))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(MockMvcResultMatchers.header().string(HeaderKeyConstants.TOTAL_COUNT, "2"));
  }

  private DiscreteCopyNumberFilter createDiscreteCopyNumberFilter() {

    List<String> sampleIds = new ArrayList<>();
    sampleIds.add(TEST_SAMPLE_STABLE_ID_1);
    sampleIds.add(TEST_SAMPLE_STABLE_ID_2);

    List<Integer> entrezGeneIds = new ArrayList<>();
    entrezGeneIds.add(TEST_ENTREZ_GENE_ID_1);
    entrezGeneIds.add(TEST_ENTREZ_GENE_ID_2);

    DiscreteCopyNumberFilter discreteCopyNumberFilter = new DiscreteCopyNumberFilter();
    discreteCopyNumberFilter.setEntrezGeneIds(entrezGeneIds);
    discreteCopyNumberFilter.setSampleIds(sampleIds);
    return discreteCopyNumberFilter;
  }

  private List<DiscreteCopyNumberData> createExampleDiscreteCopyNumberData() {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList = new ArrayList<>();
    DiscreteCopyNumberData discreteCopyNumberData1 = new DiscreteCopyNumberData();
    discreteCopyNumberData1.setMolecularProfileId(TEST_MOLECULAR_PROFILE_STABLE_ID_1);
    discreteCopyNumberData1.setSampleId(TEST_SAMPLE_STABLE_ID_1);
    discreteCopyNumberData1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1);
    discreteCopyNumberData1.setAlteration(TEST_ALTERATION_1);
    discreteCopyNumberDataList.add(discreteCopyNumberData1);
    discreteCopyNumberData1.setAnnotationJson(TEST_ANNOTATION_JSON_1);
    DiscreteCopyNumberData discreteCopyNumberData2 = new DiscreteCopyNumberData();
    discreteCopyNumberData2.setMolecularProfileId(TEST_MOLECULAR_PROFILE_STABLE_ID_2);
    discreteCopyNumberData2.setSampleId(TEST_SAMPLE_STABLE_ID_2);
    discreteCopyNumberData2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2);
    discreteCopyNumberData2.setAlteration(TEST_ALTERATION_2);
    discreteCopyNumberDataList.add(discreteCopyNumberData2);
    return discreteCopyNumberDataList;
  }

  private List<DiscreteCopyNumberData> createExampleDiscreteCopyNumberDataWithGenes() {

    List<DiscreteCopyNumberData> discreteCopyNumberDataList = createExampleDiscreteCopyNumberData();
    Gene gene1 = new Gene();
    gene1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1);
    gene1.setHugoGeneSymbol(TEST_HUGO_GENE_SYMBOL_1);
    gene1.setType(TEST_TYPE_1);
    discreteCopyNumberDataList.get(0).setGene(gene1);
    Gene gene2 = new Gene();
    gene2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2);
    gene2.setHugoGeneSymbol(TEST_HUGO_GENE_SYMBOL_2);
    gene2.setType(TEST_TYPE_2);
    discreteCopyNumberDataList.get(1).setGene(gene2);
    return discreteCopyNumberDataList;
  }
}
